This list of RNA structure prediction software is a compilation of software tools and web portals used for
RNA structure
Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quatern ...
prediction.
Single sequence secondary structure prediction.
Single sequence tertiary structure prediction
Comparative methods
The single sequence methods mentioned above have a difficult job detecting a small sample of reasonable secondary structures from a large space of possible structures. A good way to reduce the size of the space is to use evolutionary approaches. Structures that have been conserved by evolution are far more likely to be the functional form. The methods below use this approach.
RNA solvent accessibility prediction
Intermolecular interactions: RNA-RNA
Many
ncRNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-c ...
s function by binding to other
RNA
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
s. For example,
miRNA
MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides. Found in plants, animals and some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miRN ...
s regulate protein coding gene expression by binding to
3' UTRs,
small nucleolar RNAs guide post-transcriptional modifications by binding to
rRNA
Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosoma ...
,
U4 spliceosomal RNA
The U4 small nuclear Ribo-Nucleic Acid (U4 snRNA) is a non-coding RNA component of the major or U2-dependent spliceosome – a eukaryotic molecular machine involved in the splicing of pre-messenger RNA (pre-mRNA). It forms a duplex with U6, an ...
and
U6 spliceosomal RNA
U6 snRNA is the non-coding small nuclear RNA (snRNA) component of U6 snRNP (''small nuclear ribonucleoprotein''), an RNA-protein complex that combines with other snRNPs, unmodified pre-mRNA, and various other proteins to assemble a spliceosome, a ...
bind to each other forming part of the
spliceosome
A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs (snRNA) and numerous proteins. Small nuclear RNA (snRNA) molecules bind to specifi ...
and many small bacterial RNAs regulate gene expression by antisense interactions E.g.
GcvB,
OxyS and
RyhB
RyhB RNA is a 90 nucleotide RNA that down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur ( Ferric uptake regulator).
Discovery
The gene ...
.
Intermolecular interactions: MicroRNA:any RNA
The below table includes interactions that are not limited to UTRs.
Intermolecular interactions: MicroRNA:UTR
MicroRNAs
MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides. Found in plants, animals and some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miR ...
regulate protein coding gene expression by binding to
3' UTRs, there are tools specifically designed for predicting these interactions. For an evaluation of target prediction methods on high-throughput experimental data see (Baek ''et al.'', Nature 2008),
(Alexiou ''et al.'', Bioinformatics 2009),
or (Ritchie et al., Nature Methods 2009)
ncRNA gene prediction software
Family specific gene prediction software
RNA homology search software
Benchmarks
Alignment viewers, editors
Inverse folding, RNA design
;Notes:
Secondary structure viewers, editors
See also
*
RNA
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
*
Non-coding RNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-c ...
*
RNA structure
Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quatern ...
*
Comparison of nucleic acid simulation software
This is a list of notable computer programs that are used for nucleic acid
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: ...
*
Comparison of software for molecular mechanics modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
See also
*Car–Parrinello molecular dynamics
*Comparison of force-field implementations
*Comparison of nucleic acid simulation software
* ...
References
{{DEFAULTSORT:List Of Rna Structure Prediction Software
RNA structure
Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quatern ...
RNA structure prediction software
RNA
Structural bioinformatics software